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Human vs Rat LastZ alignments

Human (Homo sapiens, GRCh37) and Rat (Rattus norvegicus, Rnor_5.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 70. Human was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

Human Rat
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 1,461,159

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 2,141,118,004 out of 3,098,825,702
Covered: 957,707,698 out of 3,098,825,702

Uncovered: 1,617,335 out of 35,313,516
Matches: 27,788,340 out of 35,313,516
Mismatches: 5,500,550 out of 35,313,516
Insertions: 407,291 out of 35,313,516

Rattus norvegicus

Uncovered: 2,035,635,793 out of 2,909,698,938
Covered: 874,063,145 out of 2,909,698,938

Uncovered: 4,450,687 out of 34,224,882
Matches: 24,962,648 out of 34,224,882
Mismatches: 4,659,446 out of 34,224,882
Insertions: 152,101 out of 34,224,882